| Parameters | Input values |
|---|---|
| Folder name : | Example data |
| Sequence name : | Test sequence |
| Reference genome : | BSgenome.Hsapiens.UCSC.hg19 |
| Type of experiment : | Direct-BSP |
| Group order : | group1, group2 |
| Date of analysis : | 2022-05-18 13:03 |
| Parameters | Data files content |
|---|---|
| Sequence name : | Test sequence |
| Collections : | collection1, collection2 |
| Groups : | group1, group2 |
| Replicates : | 1, 2, 3 |
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection1_group1_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection1_group1_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection1_group1_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection1_group2_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection1_group2_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection1_group2_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection2_group1_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection2_group1_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection2_group1_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection2_group2_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection2_group2_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test
sequence/individual_results_direct/data/Test
sequence_collection2_group2_3_methdata.csv
| chr16:68770595-68770596 | chr16:68770613-68770614 | chr16:68770646-68770647 | chr16:68770665-68770666 | chr16:68770670-68770671 | chr16:68770717-68770718 | Mean | SD | |
|---|---|---|---|---|---|---|---|---|
| collection1 group1 1 | 38.44 | 21.17 | 5.56 | 24.31 | 0.00 | 12.61 | 17.02 | 13.93 |
| collection1 group1 2 | 18.65 | 12.84 | 16.93 | 19.07 | 0.00 | 20.09 | 14.60 | 7.59 |
| collection1 group1 3 | 6.12 | 8.25 | 24.85 | 6.69 | 32.95 | 16.63 | 15.92 | 11.05 |
| collection1 group2 1 | 67.41 | 83.83 | 84.18 | 85.67 | 100.00 | 74.04 | 82.52 | 11.14 |
| collection1 group2 2 | 55.41 | 75.91 | 60.26 | 52.01 | 100.00 | 67.33 | 68.49 | 17.66 |
| collection1 group2 3 | 98.62 | 65.18 | 56.78 | 82.81 | 70.73 | 90.10 | 77.37 | 15.87 |
| collection2 group1 1 | 21.60 | 13.38 | 24.98 | 31.74 | 4.84 | 20.58 | 19.52 | 9.36 |
| collection2 group1 2 | 38.62 | 0.00 | 52.73 | 16.17 | 36.61 | 0.00 | 24.02 | 21.96 |
| collection2 group1 3 | 19.37 | 3.66 | 43.99 | 4.87 | 33.12 | 25.27 | 21.71 | 15.84 |
| collection2 group2 1 | 61.26 | 63.68 | 83.57 | 71.25 | 56.68 | 93.89 | 71.72 | 14.37 |
| collection2 group2 2 | 62.96 | 91.07 | 86.62 | 61.63 | 78.68 | 80.02 | 76.83 | 12.13 |
| collection2 group2 3 | 72.37 | 65.22 | 70.84 | 82.10 | 81.23 | 66.92 | 73.11 | 7.11 |
| chr16:68770595-68770596 | chr16:68770613-68770614 | chr16:68770646-68770647 | chr16:68770665-68770666 | chr16:68770670-68770671 | chr16:68770717-68770718 | Mean | SD | |
|---|---|---|---|---|---|---|---|---|
| collection1 group1 | 21.07 | 14.09 | 15.78 | 16.69 | 10.98 | 16.44 | 15.84 | 3.32 |
| collection1 group2 | 73.81 | 74.97 | 67.07 | 73.50 | 90.24 | 77.16 | 76.12 | 7.69 |
| collection2 group1 | 26.53 | 5.68 | 40.57 | 17.59 | 24.86 | 15.28 | 21.75 | 11.87 |
| collection2 group2 | 65.53 | 73.32 | 80.34 | 71.66 | 72.20 | 80.28 | 73.89 | 5.67 |
| CpG number | CpG coordinate | Collection | Group | N | Methylation mean | SD | SEM | Confidence interval of 95% (±) |
|---|---|---|---|---|---|---|---|---|
| 1 | chr16:68770595-68770596 | collection1 | group1 | 3 | 21.07 | 16.30 | 9.41 | 40.48 |
| 1 | chr16:68770595-68770596 | collection1 | group2 | 3 | 73.81 | 22.31 | 12.88 | 55.41 |
| 1 | chr16:68770595-68770596 | collection2 | group1 | 3 | 26.53 | 10.53 | 6.08 | 26.16 |
| 1 | chr16:68770595-68770596 | collection2 | group2 | 3 | 65.53 | 5.98 | 3.46 | 14.87 |
| 2 | chr16:68770613-68770614 | collection1 | group1 | 3 | 14.09 | 6.55 | 3.78 | 16.27 |
| 2 | chr16:68770613-68770614 | collection1 | group2 | 3 | 74.97 | 9.36 | 5.40 | 23.25 |
| 2 | chr16:68770613-68770614 | collection2 | group1 | 3 | 5.68 | 6.91 | 3.99 | 17.18 |
| 2 | chr16:68770613-68770614 | collection2 | group2 | 3 | 73.32 | 15.39 | 8.88 | 38.23 |
| 3 | chr16:68770646-68770647 | collection1 | group1 | 3 | 15.78 | 9.70 | 5.60 | 24.09 |
| 3 | chr16:68770646-68770647 | collection1 | group2 | 3 | 67.07 | 14.92 | 8.61 | 37.05 |
| 3 | chr16:68770646-68770647 | collection2 | group1 | 3 | 40.57 | 14.19 | 8.19 | 35.25 |
| 3 | chr16:68770646-68770647 | collection2 | group2 | 3 | 80.34 | 8.37 | 4.83 | 20.79 |
| 4 | chr16:68770665-68770666 | collection1 | group1 | 3 | 16.69 | 9.05 | 5.22 | 22.48 |
| 4 | chr16:68770665-68770666 | collection1 | group2 | 3 | 73.50 | 18.66 | 10.78 | 46.36 |
| 4 | chr16:68770665-68770666 | collection2 | group1 | 3 | 17.59 | 13.49 | 7.79 | 33.51 |
| 4 | chr16:68770665-68770666 | collection2 | group2 | 3 | 71.66 | 10.24 | 5.91 | 25.44 |
| 5 | chr16:68770670-68770671 | collection1 | group1 | 3 | 10.98 | 19.02 | 10.98 | 47.26 |
| 5 | chr16:68770670-68770671 | collection1 | group2 | 3 | 90.24 | 16.90 | 9.76 | 41.98 |
| 5 | chr16:68770670-68770671 | collection2 | group1 | 3 | 24.86 | 17.42 | 10.06 | 43.28 |
| 5 | chr16:68770670-68770671 | collection2 | group2 | 3 | 72.20 | 13.50 | 7.79 | 33.53 |
| 6 | chr16:68770717-68770718 | collection1 | group1 | 3 | 16.44 | 3.74 | 2.16 | 9.30 |
| 6 | chr16:68770717-68770718 | collection1 | group2 | 3 | 77.16 | 11.70 | 6.76 | 29.07 |
| 6 | chr16:68770717-68770718 | collection2 | group1 | 3 | 15.28 | 13.44 | 7.76 | 33.39 |
| 6 | chr16:68770717-68770718 | collection2 | group2 | 3 | 80.28 | 13.49 | 7.79 | 33.50 |
| Collection | Group | N | Methylation mean | SD | SEM | Confidence interval of 95% (±) |
|---|---|---|---|---|---|---|
| collection1 | group1 | 3 | 15.85 | 1.21 | 0.70 | 3.01 |
| collection1 | group2 | 3 | 76.13 | 7.10 | 4.10 | 17.63 |
| collection2 | group1 | 3 | 21.75 | 2.25 | 1.30 | 5.59 |
| collection2 | group2 | 3 | 73.89 | 2.64 | 1.53 | 6.56 |
Student’s T test (two-samples, unpaired)
| CpG number | CpG coordinate | Collection | Compared group 1 | Compared group 2 | N group 1 | N group 2 | p-value | p-value significance level |
|---|---|---|---|---|---|---|---|---|
| 1 | chr16:68770595-68770596 | collection1 | group1 | group2 | 3 | 3 | 0.03390 | * |
| 2 | chr16:68770613-68770614 | collection1 | group1 | group2 | 3 | 3 | 0.00127 | ** |
| 3 | chr16:68770646-68770647 | collection1 | group1 | group2 | 3 | 3 | 0.01110 | * |
| 4 | chr16:68770665-68770666 | collection1 | group1 | group2 | 3 | 3 | 0.01930 | * |
| 5 | chr16:68770670-68770671 | collection1 | group1 | group2 | 3 | 3 | 0.00594 | ** |
| 6 | chr16:68770717-68770718 | collection1 | group1 | group2 | 3 | 3 | 0.00741 | ** |
| 1 | chr16:68770595-68770596 | collection2 | group1 | group2 | 3 | 3 | 0.00981 | ** |
| 2 | chr16:68770613-68770614 | collection2 | group1 | group2 | 3 | 3 | 0.00784 | ** |
| 3 | chr16:68770646-68770647 | collection2 | group1 | group2 | 3 | 3 | 0.02140 | * |
| 4 | chr16:68770665-68770666 | collection2 | group1 | group2 | 3 | 3 | 0.00640 | ** |
| 5 | chr16:68770670-68770671 | collection2 | group1 | group2 | 3 | 3 | 0.02280 | * |
| 6 | chr16:68770717-68770718 | collection2 | group1 | group2 | 3 | 3 | 0.00410 | ** |
Student’s T test (two-samples, unpaired)
| Collection | Compared group 1 | Compared group 2 | N group 1 | N group 2 | p-value | p-value significance level |
|---|---|---|---|---|---|---|
| collection1 | group1 | group2 | 3 | 3 | 3.74e-03 | ** |
| collection2 | group1 | group2 | 3 | 3 | 1.61e-05 | **** |
Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.
The p-values and p-value significance levels are determined by Student’s T tests (unpaired).
Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.
The p-values and p-value significance levels are determined by Student’s T tests (unpaired).
Each points represent the methylation mean of clones or replicates
for a given CpG site.
The p-values and p-value significance levels are determined by
Kruskal-Wallis tests.
legend_methylation_gradient.png
genomic_replicates_by-group.png
lollipop_groups_as-is_condensed.png
lollipop_groups_as-is_proportional.png
lollipop_groups_by-group_condensed.png
lollipop_groups_by-group_proportional.png
lollipop_groups_by-meth_condensed.png
lollipop_groups_by-meth_proportional.png
lollipop_groups_clust_condensed.png
lollipop_groups_clust_proportional.png
lollipop_replicates_as-is_condensed.png
lollipop_replicates_as-is_proportional.png
lollipop_replicates_by-group_condensed.png
lollipop_replicates_by-group_proportional.png
lollipop_replicates_by-meth_condensed.png
lollipop_replicates_by-meth_proportional.png
meth_profile_collection1_condensed_psign.png
meth_profile_collection1_condensed_pval.png
meth_profile_collection1_proportional_psign.png
meth_profile_collection1_proportional_pval.png
meth_profile_collection2_condensed_psign.png
meth_profile_collection2_condensed_pval.png